Detection of insertion/deletions (indels) of the <i>ATBF1</i> gene and their effects on growth-related traits in three indigenous goat breeds

Abstract. The AT motif-binding factor (ATBF1), also known as zinc finger homeobox 3 (ZFXH3), is necessary for activating the POU1F1 gene; thus, the ATBF1 gene greatly affects the grow traits in animals. The objective of this work was to explore novel indel (insertion/deletion) variations and their associations with growth traits in three native Chinese goat breeds. Two indels within the ATBF1 gene were found in the Shaanbei white cashmere goat (SWCG; n=581), the Guanzhong dairy goat (GZDG; n=334) and the Hainan black goat (HNBG; n=270) for the first time using 12 pairs of primers. Association analysis revealed that the P1-12-bp indel was consistently correlated with the body height of the three breeds, and individuals with ID (insertion/deletion) and DD (deletion/deletion) genotypes had a higher body weight than the II (insertion/insertion) genotype (P=0.036); the P11-6-bp indel was consistently correlated with chest circumference and hip width of the three breeds. Moreover, these two loci were associated with other several growth-related traits in different breeds. Hence, these findings indicated that the goat ATBF1 gene had marked effects on growth traits and the growth-trait-related loci, which would contribute to improving the growth-related traits of local breeds in the goat industry by implementing marker-assisted selection (MAS).

Detection of Insertions/Deletions Within SIRT1, SIRT2 and SIRT3 Genes and Their Associations with Body Measurement Traits in Cattle

Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P < 0.05 or P < 0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.

A novel 12 bp deletion within goat <i>LHX4</i> gene significantly affected litter size

Abstract. The LIM homeobox transcription factor 4 (LHX4) gene plays a critical role in regulating the development of the pituitary and the secretion of growth hormone (GH) and prolactin (PRL) associated with reproduction. Thus this gene may affect litter size. Herein, the aim of this study is to detect the novel insertion/deletion (indel) within the LHX4 gene as well as to test its association with litter size in 1149 Shaanbei white cashmere goats. Herein, a novel 12 bp indel (NC_030823.1:g.60001011_60001022delGGGGAGGAGGGG) was firstly found, which was located in the first intron. Meanwhile, three genotypes were detected in Shaanbei white cashmere goats, and the allelic frequencies of I and D were 0.593 and 0.407, respectively. Interestingly, the genotype distributions between mothers of single-lamb (n = 895) and multi-lamb (n = 254) groups within Shaanbei white cashmere goats were significantly different, implying that the 12 bp indel might affect the litter size. Furthermore, the association analysis was carried out to find out that the 12 bp indel was significantly associated with litter size in the analyzed goat population (P  <  0.05). The litter sizes of genotype DD and ID individuals were superior to those of genotype II (P  <  0.05). These findings suggest that this locus could be considered as a genetic marker for goat breeding, enriching the research category of functional genome of goats.